Ok, so I've had SOME experience with this stuff, and unfortunately the same technique I used for another game, Borderlands, doesn't work. I use Auto Window Manager, give them both a new rule to Stay on Top, and wait until they both become active windows. Sadly, it didn't work. How I'm running two copies at once is I used Sandboxie, which some of you may be more familiar with than me, and I created the Halo2 Sandboxie, allowed Admin rights, set file access on "%personal%\My Games\Halo CE\" without the quotes, and "C:Users\My Name\Downloads\Installation Programs\HaloCEinstaller" (note the installer has a much more complicated name I copy and pasted into there, but that I simplified it for this). Then, I made a batch file made like this:
"C:\Program Files\Sandboxie\Start.exe" /elevate /box:Halo2 "C:\Program Files (x86)\Microsoft Games\Halo Custom Edition\haloce.exe" -nolauncher -AlwaysFocus -Windowed -WindowPosX=0
It starts Halo CE, but Halo CE gets mad because:
"Cannot find user 'C:\Users\My Name\Desktop\config.txt'"
I can run both copies of Halo CE, one with Sandboxie regular startup, and outside of Sandboxie again with regular startup, no batch files or anything. I cannot keep them both active with my Auto Window Manager though. I need to find out how to do this. Thanks if you can offer help.

Forgive me for asking but why would you need 2 active instances of halo running on the same pc?

Me and my brother are going to play together.

make a [symbolic link] that points to the real config.txt

Where is that/how do I do it?

EDIT:
I know where the config.txt is, I don't know what to do now. What other code do I have to write into there? Both files are in C:\Program Files (86x)\Microsoft Games\Halo Custom Edition\" But then what? What do I do to put it in there?
Edited by Dark_Novak on Oct 2, 2012 at 04:37 PM

I just realized, that since config.txt is just a text file, why not just copy it to the desktop :)

Any special commands I have to input to tell it "Activate config"?

EDIT: I did that. Then I couldn't run the normal Halo CE because it couldn't find the files where it wanted to find it, so after I copied the files from Halo CE folder to desktop, then normal Halo CE was complaining about not having access to My Documents. It'd be easier to tell it to look at the Halo CE folder.
Edited by Dark_Novak on Oct 2, 2012 at 07:31 PM

The problem with that would be using both profiles at once wouldn't it? I'm assuming by profile you mean like mine is Dark_Novak, or i could log into SparklePants the 3rd? Another user on the computer?

EDIT: Just typed in -multiple into the target field, and whenever I start Halo Custom Edition then double click the icon again, it just reopens the one that is already open.
Edited by Dark_Novak on Oct 4, 2012 at 06:19 PM

-multiple is not a command in the target field. Of course it will not work :/

I'm pretty sure that Halo over LAN won't work with the same machine for send and receive messages.

Then where does -multiple go?

Halo doesn't have a -multiple switch in its programming

you can try using virtual computer, but it can cause some problems... (E.G. https://www.virtualbox.org/wiki/Downloads )
Edited by afD2345 on Oct 6, 2012 at 12:49 PM